The Network Workbench (NWB) Tool(v0.2.0
release) is a network analysis, modeling and visualization toolkit for
biomedical, social science and physics research. It is a standalone desktop
application requiring JAVA 1.4+ JRE. The tool installs and runs on Windows
and Linux x86.

It is
using Cyberinfrastructure Shell
(CIShell)
v0.2.1 to integrate various datasets and algorithms. Although CIShell is developed using JAVA, it can integrate
algorithms developed by other programming languages such as FORTRAN, C, and
C++.

2.Downloading,
Installing and Uninstalling

Download
the NWB tool v0.2.0 and
make sure to save the download as a jar file.

To install the NWB tool, simply double click
the jar file, or run the command line java -jar nwb-installer_0.2.0.jar.

To uninstall the NWB tool, go to program (or application) menu, find
“Network Workbench” program group, click “Uninstall NWB”. Another option is to
go to the directory “nwb_installation_dir/Uninstaller”
and double click uninstaller.jar.

The tool provides 41 network
analysis, modeling, and visualization algorithms. Half of them are developed
using FORTRAN, while the rest of them use JAVA. Detailed algorithm descriptions
are available at the NWB
Community Wiki. Here is the complete algorithm
list in the v0.2.0 release.

Category

Algorithm

Language

Preprocessing

Directory Hierarchy Reader

JAVA

Modeling

Erdös-Rényi Random

FORTRAN

Barabási-Albert Scale-Free

FORTRAN

Watts-Strogatz Small World

FORTRAN

Chord

JAVA

CAN

JAVA

Hypergrid

JAVA

PRU

JAVA

Analysis

Attack
Tolerance

JAVA

Error
Tolerance

JAVA

Betweenness Centrality

JAVA

Site Betweenness

FORTRAN

Average
Shortest Path

FORTRAN

Connected
Components

FORTRAN

Diameter

FORTRAN

Page Rank

FORTRAN

Shortest
Path Distribution

FORTRAN

Watts-Strogatz Clustering Coefficient

FORTRAN

Watts-Strogatz Clustering Coefficient Versus Degree

FORTRAN

Directed
k-Nearest Neighbor

FORTRAN

Undirected
k-Nearest Neighbor

FORTRAN

Indegree Distribution

FORTRAN

Outdegree Distribution

FORTRAN

Node Indegree

FORTRAN

Node Outdegree

FORTRAN

One-point
Degree Correlations

FORTRAN

Undirected
Degree Distribution

FORTRAN

Node
Degree

FORTRAN

k
Random-Walk Search

JAVA

Random
Breadth First Search

JAVA

CAN
Search

JAVA

Chord
Search

JAVA

Visualization

Tree Map

JAVA

Tree Viz

JAVA

Radial Tree
/ Graph

JAVA

Kamada-Kawai

JAVA

Force
Directed

JAVA

Spring

JAVA

Fruchterman-Reingold

JAVA

Circular

JAVA

Parallel
Coordinates (demo)

JAVA

Tool

XMGrace

Table 1: A list of algorithms in the NWB Tool v0.2.0

3.3.Converters and Conversion Service

The tool provides a set of
converters and a conversion service tying them together that automatically
transforms data from one format to another. When invoked, the conversion
service will try to find a chain of converters that can transform the input
data format to one that an algorithm can accept. Figure 1 shows the conversion
graph supported by the NWB tool v0.2.0 release.

Figure
1: Conversion Graph in the NWB Tool v0.2.0

3.4.Other Features

·Sample Data: The tool provides several sample datasets in nwb_installation_dir/sampledata/Network.

·References and Documentations of Algorithms: When a user selects
an algorithm from the menu, the acknowledgement will appear in the console. The
acknowledgement information contains the original authors of the algorithm, the
developers, the integrators, a reference, and the URL to the reference if available.
Furthermore, the acknowledgement includes a URL to the algorithm description at
the NWB community wiki website at https://nwb.slis.indiana.edu/community.

4.Known Issues

This list covers some of the known
problems with NWB Tool v0.2.0. Please read this before reporting any new bugs.

·XMGrace: the tool provides a plugin that can invoke xmgrace
--- a WYSIWYG 2D plotting tool to plot analysis results. This plugin exclusively works in the Linux
environment. In order for the plugin to work, the
tool requires a working installation of the Grace package.

·Visualization Algorithms: All visualization algorithms except the
xmgraceplugins and
Parallel Coordinates (demo) are developed using Prefuse alpha and JUNG libraries. Therefore, these
visualization algorithms do not visualize large-scale networks. To our
knowledge, it takes excessive time to visualize a graph with over 1000 nodes
and the algorithms can not handle a graph with over 5000 nodes in general.

·Algorithm Performance: Those algorithms developed in FORTRAN are
more scalable and efficient when comparing to JAVA-based implementations. They
can generate and deal with large networks with over 1,000,000 nodes.

·Stop a Running Algorithm: This release does not have a scheduler
--- a module that allows users to stop/pause/resume a running algorithm. This
feature will be implemented and delivered in the next release on December 22nd,
2006.

·Directed vs. Undirected Networks: Many analysis algorithms in
this release can only deal with undirected networks. When a user tries to apply
those algorithms to a directed network, they will generate an error messages
such as “Error! The program should be applied on directed networks.” We will make
the improvement in the next release so that algorithms that can only apply to
direct networks won’t be selectable when an undirected network is given as
input.

·Run on
Mac OS X PPC: The tool can be installed and run on Mac OS X PPC. On the
other hand, without thorough testing, there are some problems in this release.
For instance, all visualization algorithms don’t work on Mac because they use
AWT or Swing. The web page at http://www.eclipse.org/swt/faq.php#swtawtosx
explains the reason. Fileà view may or may not work depending on the platform
setup as well as null pointer exceptions when the tool starts up. We would
appreciate bug reporting by sending us the console log messages.

5.Icons

The NWB tool uses the following icons to represent different datasets: